Computational Neurobiology Group - Systems Biology of Neuronal Signalling
The interests of the group Computational Neurobiology revolve around
signal transduction in neurons, ranging from the molecular structure
of membrane proteins involved in neurotransmission to modelling
signalling pathways. A strong focus is the molecular and cellular
basis of neuroadaptation in neurons of the basal ganglia. We also
provide services that facilitate our research, including database
production and software development.
The Systems
Biology Markup Language (SBML) is designed to facilitate the
exchange of biological models between different types of
software. Involved in the development of SBML since the origin of the
project, we are working on the language extensions and developing
software that supports SBML. Moving from the form to the content, we
are also developing standards for model curation and annotation, and
controlled vocabularies to increase the information content of models.
However well a model is designed, it is useful only if potential
users can access it. BioModels Database is a data resource that allows biologists to store,
search and retrieve published mathematical models of biological
interest.
A significant proportion of the proteins involved in neuronal
signalling are embedded in biological membranes. Their
three-dimensional structures are seldom known and this precludes a
clear understanding of their function. The European Membrane Protein Consortium
focusses on solving the bottlenecks that prevent the high-throughput
determination of their structures.
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November 20th 2007
We are pleased to announce that the UK Biotechnology and Biological Sciences Research council (BBSRC) accepted to fund the long term development of BioModels Database through its Bioinformatics and Biological Resources Fund. The BBRF will support a curator and half a developer during four years.
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 | September 25th 2007
We are pleased to
announce the ninth release of BioModels Database. This new release sees the the addition of
47 models, including 38 in the curated branch, bringing BioModels Database to
12482 reactions. …more |
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June 15th 2007
SBML editors are pleased to announce the public release of SBML Level 2 Version 3. The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others …more |
Ligand-Gated Ion Channel database 60th Release
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June 06th 2007
We are pleased to announce the 60th release of the Ligand-Gated Ion Channel database. For this release 18 entries have been added, and four entries have been updated. Mouse, rat, and human LGIC entries in the database are now completed to current knowledge. |
| June 05th 2007
We are pleased to
announce the eighth release of BioModels Database,
dedicated to Reinhart Heinrich, one of the fathers of Systems Biology. This new release sees the the addition of
34 models, including 27 in the curated branch, bringing BioModels Database to
7684 reactions. …more |
BioModels Database ranked first data resource in Systems Biology
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April 17st 2007
BioModels Database was ranked first database used in Systems Biology by a survey published this month in Nature Biotechnology. It is ranked third in the list of 95 specialised tools (the first two being libSBML and CellDesigner). SBMLeditor is also in the list (15th position) as well as StochSim (30th position).
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BBSRC funds collaboration with Japanese partners
| January 05th 2007
We are pleased to
announce the seventh release of BioModels Database,
the "DOQCS release". As the nickname of this release
indicates, this is the first one incorporating models
coming from the Database of Quantitative Cellular
Signalling. This new release sees the the addition of
16 models in the curated branch, and 26 in the
non-curated branch, bringing BioModels Database to
6458 reactions. …more |
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December 04th 2006
The BioModels
Database, hosted by the European Molecular Biology
Laboratory's European Bioinformatics Institute
(EMBL-EBI) in Cambridge, UK, has entered a formal
data-exchange agreement with the Database of
Quantitative Chemical Signalling (DOQCS) of the
National Centre for Biological Sciences (NCBS) in
Bangalore, India. Both data resources will now simultaneously
release computer models of biological
processes to the community. This agreement is the culmination
of more than a year's work to make the models
in DOQCS available in Systems Biology Markup
Language (SBML). The agreement will provide users
of both databases with a larger pool of models, whilst
giving them the freedom to use the different interfaces
and tools associated with each resource. …more |
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November 06th 2006
Projecting neurons of the striatum are a crucial relay of the basal
ganglia, involved in motor, psycho-motor and behavioural functions.
We present a detailed
quantitative model of the integration of dopamine and glutamate signals by the protein DARPP-32. Dynamic simulations show that the
function of DARPP-32 depends on the delay between the two signals, and
therefore the protein not only measures the intensity, but also the
coincidence between signals. …more |
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October 03th 2006
We are pleased to announce the sixth release of BioModels
Database. It sees the addition of 42 models that represent 3584 reactions. A new branch has been added to distribute non-curated models…more |
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September 26th 2006
We are pleased to announce the public release of SBML Level 2 Version 2. The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others …more |
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June 05th 2006
We are pleased to announce the fifth release of BioModels
Database. It sees the addition of 4 models that represent 144 reactions. New export formats include BioPAX and SVG graphs …more |
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February 28th 2006
The first BioModels.net training camp will be held at the The European
Bioinformatics Institute between the 10th and 12th April 2006 …more |
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January 31st 2006
We are pleased to announce the fourth release of BioModels
Database. It sees the addition of 6 models that represent 220
reactions, the biggest increase since the creation of the
resource. Most importantly, this release introduces the qualification
of annotations, following the recommendation of the MIRIAM
standard …more |
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December 7th 2005
Scientists from 14 different organisations
including the EMBL-European Bioinformatics Institute annouce MIRIAM, a
new quality standard for biochemical models, in the 6 December issue of Nature Biotechnology. MIRIAM will help researchers to reuse, modify and
combine computer models of biochemical processes to gain a fuller
understanding of life at the molecular and cellular level…more |
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Apr 11th 2005
BioModels Database, the world's first database of
curated and annotated biological models, is launched today. BioModels Database is the result
of a collaboration led by the EBI and the SBML Team, an international
group that develops open-source standards to describe biological
systems... more |
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5th April 2005
The Computational Neurobiology Group is organising a workshop in "Systems Biology of Neuroadaptation in Mesotelencephalic Dopamine Pathways"... more |
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26th Aug 2004
The Computational Neurobiology group have launched a Fasta for the Ligand Gated Ion Channel (LGIC) database... more |
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